AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination

• Published in: Nucleic acids research Vol. 46; no. W1; pp. W479 - W485
• Main Authors: Medlar, Alan J, Törönen, Petri, Holm, Liisa
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 02.07.2018
• Subjects: Amino Acid Sequence; Animals; Bacterial Proteins - classification; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Chlamydia trachomatis - classification; Chlamydia trachomatis - genetics; Chlamydia trachomatis - isolation & purification; Erwinia - classification; Erwinia - genetics; Erwinia - isolation & purification; Gene Expression; Genomics - methods; Heteroptera - microbiology; Internet; Molecular Sequence Annotation; Phylogeny; Proteome - classification; Proteome - genetics; Proteome - metabolism; Sequence Homology, Amino Acid; Software; Symbiosis - physiology; Thysanoptera - microbiology; Web Server Issue
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gky359

Abstract We present AAI-profiler, a web server for exploratory analysis and quality control in comparative genomics. AAI-profiler summarizes proteome-wide sequence search results to identify novel species, assess the need for taxonomic reclassification and detect multi-isolate and contaminated samples. AAI-profiler visualises results using a scatterplot that shows the Average Amino-acid Identity (AAI) from the query proteome to all similar species in the sequence database. Taxonomic groups are indicated by colour and marker styles, making outliers easy to spot. AAI-profiler uses SANSparallel to perform high-performance homology searches, making proteome-wide analysis possible. We demonstrate the efficacy of AAI-profiler in the discovery of a close relationship between two bacterial symbionts of an omnivorous pirate bug (Orius) and a thrip (Frankliniella occidentalis), an important pest in agriculture. The symbionts represent novel species within the genus Rosenbergiella so far described only in floral nectar. AAI-profiler is easy to use, the analysis presented only required two mouse clicks and was completed in a few minutes. AAI-profiler is available at http://ekhidna2.biocenter.helsinki.fi/AAI.